MiMeDB: Showing metabocard for Obafluorin (MMDBc0003563)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-05-14 21:33:18 UTC

Update Date

2025-10-07 16:04:45 UTC

Metabolite ID

MMDBc0003563

Metabolite Identification

Common Name

Obafluorin

Description

Obafluorin is a natural antibiotic belonging to the chemical class of β-lactone derivatives. It acts as a novel covalent inhibitor of threonyl-tRNA synthetase (ThrRS), a crucial enzyme in protein synthesis. The overall structure of obafluorin is reminiscent of the β-lactone-forming thioesterase domain, which is integral to its biosynthesis (PMID:38908753 ; PMID:38617275 ). The catechol moiety of obafluorin is critical for its antibacterial activity, as it plays a significant role in the compound's bioactivity (PMID:37920400 ). Research indicates that the catechol coordinates with Zn2+ in the ThrRS active site, although obafluorin itself is a weak Zn2+ binder and shows a strong interaction with Fe3+ (PMID:37920400 ). This interaction enhances its antibacterial efficacy, particularly in the presence of Fe3+, suggesting that obafluorin does not function as a Trojan horse antibiotic but rather benefits from metal-mediated uptake (PMID:37920400 ). The synthesis of obafluorin analogues through mutasynthesis and the investigation of its interactions with metal ions further elucidate its biological mechanisms and potential applications in combating bacterial infections (PMID:37920400 ).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305142123332D          

 28 30  0  0  1  0            999 V2000
   -2.1434    6.5292    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    5.7042    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    6.9417    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9314    3.3603    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6939    4.0748    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3439    4.0748    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1064    4.7893    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6939    2.6459    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1064    3.3603    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9314    4.7893    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    5.2917    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    6.5292    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1311    2.6459    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145    3.2292    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7145    5.7042    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    4.4667    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2978    2.6459    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    4.0542    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3439    5.5037    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    6.9417    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    5.2917    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    4.0542    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1228    2.6459    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9314    6.2182    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1689    5.5037    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1846    3.4081    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4767    3.5449    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  3  1  1  0  0  0  0
  6  4  1  0  0  0  0
  7  5  2  0  0  0  0
  9  4  2  0  0  0  0
  9  5  1  0  0  0  0
  9  8  1  0  0  0  0
 10  6  2  0  0  0  0
 10  7  1  0  0  0  0
 11  2  1  0  0  0  0
 12  3  2  0  0  0  0
 13  8  1  1  0  0  0
 14 13  1  0  0  0  0
 15 11  2  0  0  0  0
 15 12  1  0  0  0  0
 16 11  1  0  0  0  0
 17 14  1  0  0  0  0
 14 18  1  1  0  0  0
 18 16  2  0  0  0  0
 19 10  1  0  0  0  0
 20 12  1  0  0  0  0
 21 15  1  0  0  0  0
 16 22  1  4  0  0  0
 23 17  2  0  0  0  0
 24 19  2  0  0  0  0
 25 19  2  0  0  0  0
 26 13  1  0  0  0  0
 26 17  1  0  0  0  0
 13 27  1  6  0  0  0
 14 28  1  6  0  0  0
M  END


  Mrv1652305142123332D          

 28 30  0  0  1  0            999 V2000
   -2.1434    6.5292    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    5.7042    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    6.9417    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9314    3.3603    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6939    4.0748    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3439    4.0748    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1064    4.7893    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6939    2.6459    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1064    3.3603    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9314    4.7893    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    5.2917    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    6.5292    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1311    2.6459    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145    3.2292    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7145    5.7042    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    4.4667    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2978    2.6459    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    4.0542    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3439    5.5037    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    6.9417    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    5.2917    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    4.0542    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1228    2.6459    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9314    6.2182    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1689    5.5037    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1846    3.4081    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4767    3.5449    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  3  1  1  0  0  0  0
  6  4  1  0  0  0  0
  7  5  2  0  0  0  0
  9  4  2  0  0  0  0
  9  5  1  0  0  0  0
  9  8  1  0  0  0  0
 10  6  2  0  0  0  0
 10  7  1  0  0  0  0
 11  2  1  0  0  0  0
 12  3  2  0  0  0  0
 13  8  1  1  0  0  0
 14 13  1  0  0  0  0
 15 11  2  0  0  0  0
 15 12  1  0  0  0  0
 16 11  1  0  0  0  0
 17 14  1  0  0  0  0
 14 18  1  1  0  0  0
 18 16  2  0  0  0  0
 19 10  1  0  0  0  0
 20 12  1  0  0  0  0
 21 15  1  0  0  0  0
 16 22  1  4  0  0  0
 23 17  2  0  0  0  0
 24 19  2  0  0  0  0
 25 19  2  0  0  0  0
 26 13  1  0  0  0  0
 26 17  1  0  0  0  0
 13 27  1  6  0  0  0
 14 28  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0003563

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]1(CC2=CC=C(C=C2)N(=O)=O)OC(=O)[C@@]1([H])N=C(O)C1=C(O)C(O)=CC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C17H14N2O7/c20-12-3-1-2-11(15(12)21)16(22)18-14-13(26-17(14)23)8-9-4-6-10(7-5-9)19(24)25/h1-7,13-14,20-21H,8H2,(H,18,22)/t13-,14+/m1/s1

> <INCHI_KEY>
AINNQKIVZOTQBB-KGLIPLIRSA-N

> <FORMULA>
C17H14N2O7

> <MOLECULAR_WEIGHT>
358.306

> <EXACT_MASS>
358.080100799

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
40

> <JCHEM_AVERAGE_POLARIZABILITY>
33.93779878083545

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2,3-dihydroxy-N-[(2R,3S)-2-[(4-nitrophenyl)methyl]-4-oxooxetan-3-yl]benzene-1-carboximidic acid

> <ALOGPS_LOGP>
2.37

> <JCHEM_LOGP>
3.5872299500000002

> <ALOGPS_LOGS>
-3.75

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.48216780200248

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.885140313679394

> <JCHEM_PKA_STRONGEST_BASIC>
-0.7492663718008002

> <JCHEM_POLAR_SURFACE_AREA>
145.17

> <JCHEM_REFRACTIVITY>
89.50909999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.42e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2,3-dihydroxy-N-[(2R,3S)-2-[(4-nitrophenyl)methyl]-4-oxooxetan-3-yl]benzenecarboximidic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 14-MAY-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   14-MAY-21         0                                  
HETATM    1  C   UNK     0      -4.001  12.188   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -4.001  10.648   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.667  12.958   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.605   6.273   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.295   7.606   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.375   7.606   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.065   8.940   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.295   4.939   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.065   6.273   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.605   8.940   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -2.667   9.878   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -1.334  12.188   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -0.245   4.939   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -1.334   6.028   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -1.334  10.648   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -2.667   8.338   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -2.423   4.939   0.000  0.00  0.00           C+0
HETATM   18  N   UNK     0      -1.334   7.568   0.000  0.00  0.00           N+0
HETATM   19  N   UNK     0       4.375  10.274   0.000  0.00  0.00           N+0
HETATM   20  O   UNK     0       0.000  12.958   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      -0.000   9.878   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      -4.001   7.568   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      -3.963   4.939   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       3.605  11.607   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       5.915  10.274   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0      -1.334   3.850   0.000  0.00  0.00           O+0
HETATM   27  H   UNK     0       0.345   6.362   0.000  0.00  0.00           H+0
HETATM   28  H   UNK     0      -2.756   6.617   0.000  0.00  0.00           H+0
CONECT    1    2    3                                                       
CONECT    2    1   11                                                       
CONECT    3    1   12                                                       
CONECT    4    6    9                                                       
CONECT    5    7    9                                                       
CONECT    6    4   10                                                       
CONECT    7    5   10                                                       
CONECT    8    9   13                                                       
CONECT    9    4    5    8                                                  
CONECT   10    6    7   19                                                  
CONECT   11    2   15   16                                                  
CONECT   12    3   15   20                                                  
CONECT   13    8   14   26   27                                             
CONECT   14   13   17   18   28                                             
CONECT   15   11   12   21                                                  
CONECT   16   11   18   22                                                  
CONECT   17   14   23   26                                                  
CONECT   18   14   16                                                       
CONECT   19   10   24   25                                                  
CONECT   20   12                                                            
CONECT   21   15                                                            
CONECT   22   16                                                            
CONECT   23   17                                                            
CONECT   24   19                                                            
CONECT   25   19                                                            
CONECT   26   13   17                                                       
CONECT   27   13                                                            
CONECT   28   14                                                            
MASTER        0    0    0    0    0    0    0    0   28    0   60    0
END

Synonyms

Not Available

Molecular Formula

C₁₇H₁₄N₂O₇

Average Mass

358.306

Monoisotopic Mass

358.080100799

IUPAC Name

2,3-dihydroxy-N-[(2R,3S)-2-[(4-nitrophenyl)methyl]-4-oxooxetan-3-yl]benzene-1-carboximidic acid

Traditional Name

2,3-dihydroxy-N-[(2R,3S)-2-[(4-nitrophenyl)methyl]-4-oxooxetan-3-yl]benzenecarboximidic acid

CAS Registry Number

Not Available

SMILES

[H][C@]1(CC2=CC=C(C=C2)N(=O)=O)OC(=O)[C@@]1([H])N=C(O)C1=C(O)C(O)=CC=C1

InChI Identifier

InChI=1S/C17H14N2O7/c20-12-3-1-2-11(15(12)21)16(22)18-14-13(26-17(14)23)8-9-4-6-10(7-5-9)19(24)25/h1-7,13-14,20-21H,8H2,(H,18,22)/t13-,14+/m1/s1

InChI Key

AINNQKIVZOTQBB-KGLIPLIRSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as n-acyl-alpha amino acids and derivatives. N-acyl-alpha amino acids and derivatives are compounds containing an alpha amino acid (or a derivative thereof) which bears an acyl group at its terminal nitrogen atom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

N-acyl-alpha amino acids and derivatives

Alternative Parents

Substituents

Alpha-amino acid ester
N-acyl-alpha amino acid or derivatives
Salicylamide
Salicylic acid or derivatives
Benzamide
Benzoic acid or derivatives
Nitrobenzene
Nitroaromatic compound
Benzoyl
Catechol
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Phenol
Monocyclic benzene moiety
Benzenoid
Vinylogous acid
Beta_propiolactone
Secondary carboxylic acid amide
Organic nitro compound
Carboxamide group
Carboxylic acid ester
Oxetane
Lactone
C-nitro compound
Organoheterocyclic compound
Propargyl-type 1,3-dipolar organic compound
Organic 1,3-dipolar compound
Allyl-type 1,3-dipolar organic compound
Oxacycle
Monocarboxylic acid or derivatives
Organic oxoazanium
Organic nitrogen compound
Carbonyl group
Organopnictogen compound
Organooxygen compound
Organic oxygen compound
Organic oxide
Organonitrogen compound
Hydrocarbon derivative
Organic zwitterion
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.064 g/L	ALOGPS
logP	2.37	ALOGPS
logP	3.59	ChemAxon
logS	-3.8	ALOGPS
pKa (Strongest Acidic)	6.89	ChemAxon
pKa (Strongest Basic)	-0.75	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	145.17 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	89.51 m³·mol⁻¹	ChemAxon
Polarizability	33.94 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Not Available

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Microbial Pathways

Pathways

This table shows at most 5 pathways. For the full list of associated pathways:

See All Associated Bacterial Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria/Eubacteria	Proteobacteria	1	Human ; Human subgingival plaque	Metabolic reconstruction

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

129096

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Obafluorin

METLIN ID

Not Available

PubChem Compound

146354

PDB ID

Not Available

ChEBI ID

Not Available

CMMC Knowledgebase

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

van Santen JA, Poynton EF, Iskakova D, McMann E, Alsup TA, Clark TN, Fergusson CH, Fewer DP, Hughes AH, McCadden CA, Parra J, Soldatou S, Rudolf JD, Janssen EM, Duncan KR, Linington RG: The Natural Products Atlas 2.0: a database of microbially-derived natural products. Nucleic Acids Res. 2022 Jan 7;50(D1):D1317-D1323. doi: 10.1093/nar/gkab941. [PubMed:34718710 ]

Showing metabocard for Obafluorin (MMDBc0003563)

MOL for #<Metabolite:0x00007fd420dea930>

3D MOL for #<Metabolite:0x00007fd420dea930>

3D SDF for #<Metabolite:0x00007fd420dea930>

3D-SDF for #<Metabolite:0x00007fd420dea930>

PDB for #<Metabolite:0x00007fd420dea930>

3D PDB for #<Metabolite:0x00007fd420dea930>

SMILES for #<Metabolite:0x00007fd420dea930>

INCHI for #<Metabolite:0x00007fd420dea930>

Structure for #<Metabolite:0x00007fd420dea930>

3D Structure for #<Metabolite:0x00007fd420dea930>